The Vienna RNA Websuite is a collection of web-based tools for RNA sequence analysis, including folding, design, and prediction of RNA-RNA interactions. It provides a web interface to the Vienna RNA package, which includes programs for RNA folding, comparison, and prediction of RNA-RNA interactions. The web server is freely accessible at http://rna.tbi.univie.ac.at/. The Vienna RNA Websuite includes several servers: RNAfold for predicting RNA secondary structures, RNAalifold for consensus structure prediction of aligned sequences, RNAinverse for sequence design based on a given structure, RNAcofold for predicting RNA-RNA interactions, RNAup for predicting RNA-RNA interactions, barriers for analyzing RNA folding kinetics, and LocARNA for structural RNA alignments. Each server offers a web interface with input fields, parameter settings, and output visualization. The servers use standard RNA energy parameters and allow users to select alternative parameters. The output includes various graphical representations, such as dot-bracket notation, dot plots, and SVG images. The servers are designed to provide a uniform interface to the Vienna RNA package. They use the standard RNA energy parameters from the Turner group and allow users to select alternative parameters. The servers are equipped with test input data and provide help pages for users. The servers also allow users to receive email notifications upon completion of their jobs. The RNAfold server predicts the minimum free energy (MFE) secondary structure of single sequences and provides base-pairing probabilities. The RNAalifold server predicts the consensus structure of aligned sequences. The RNAinverse server finds sequences that fit into a predefined secondary structure. The RNAcofold server computes the hybridization energy and base-pairing pattern of two RNA sequences. The RNAup server predicts RNA-RNA interactions. The barriers server analyzes RNA folding kinetics. The LocARNA server produces structural multiple sequence alignments of RNA sequences. The web server is implemented using Apache, Perl, BioPerl, CGI, and client-side JavaScript. It uses two Intel Core 2 Quad machines for performing calculations. The work was supported by various funding sources, including the Austrian GEN-AU projects and the European Union.The Vienna RNA Websuite is a collection of web-based tools for RNA sequence analysis, including folding, design, and prediction of RNA-RNA interactions. It provides a web interface to the Vienna RNA package, which includes programs for RNA folding, comparison, and prediction of RNA-RNA interactions. The web server is freely accessible at http://rna.tbi.univie.ac.at/. The Vienna RNA Websuite includes several servers: RNAfold for predicting RNA secondary structures, RNAalifold for consensus structure prediction of aligned sequences, RNAinverse for sequence design based on a given structure, RNAcofold for predicting RNA-RNA interactions, RNAup for predicting RNA-RNA interactions, barriers for analyzing RNA folding kinetics, and LocARNA for structural RNA alignments. Each server offers a web interface with input fields, parameter settings, and output visualization. The servers use standard RNA energy parameters and allow users to select alternative parameters. The output includes various graphical representations, such as dot-bracket notation, dot plots, and SVG images. The servers are designed to provide a uniform interface to the Vienna RNA package. They use the standard RNA energy parameters from the Turner group and allow users to select alternative parameters. The servers are equipped with test input data and provide help pages for users. The servers also allow users to receive email notifications upon completion of their jobs. The RNAfold server predicts the minimum free energy (MFE) secondary structure of single sequences and provides base-pairing probabilities. The RNAalifold server predicts the consensus structure of aligned sequences. The RNAinverse server finds sequences that fit into a predefined secondary structure. The RNAcofold server computes the hybridization energy and base-pairing pattern of two RNA sequences. The RNAup server predicts RNA-RNA interactions. The barriers server analyzes RNA folding kinetics. The LocARNA server produces structural multiple sequence alignments of RNA sequences. The web server is implemented using Apache, Perl, BioPerl, CGI, and client-side JavaScript. It uses two Intel Core 2 Quad machines for performing calculations. The work was supported by various funding sources, including the Austrian GEN-AU projects and the European Union.